I like both bands, but Dream Theater by a long shot. I'm afraid PT will always be a band that I have to be in the right mood to listen to, whereas Dream Theater have several albums I can throw on at anytime.
This is how I decided:
My two favorite Dream Theater albums,
Awake and
Images and Words, slay my two favorite Porcupine Tree albums,
In Absentia and
Deadwing, regardless of how you match them up.
My favorite mid-tier Dream Theater album,
Black Clouds and Silver Linings, is a little bit better than my favorite mid-tier Porcupine Tree album,
Fear of a Blank Planet.
And, finally, the worst of the Dream Theater discography,
Systematic Chaos, is still more interesting to me than the worst of the Porcupine Tree discography,
The Incident.
So there ya go.